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Step 1 of 10

Write Your Kickoff Prompt

4of 10~10 min
  • Multi-agent prompt design
  • How to seed productive disagreement
  • Using corpus excerpts for grounding
What you'll do
  • Choose a research question
  • Build a corpus excerpt
  • Write the kickoff prompt

The kickoff prompt is what seeds all three agents with your research question and relevant context. A well-crafted kickoff leads to productive disagreement; a vague one leads to generic convergence.

1Choose Your Research Question

Good research questions are discriminative: different answers would lead to different actions (experiments, decisions, models).

Good Example

"What determines whether a cell becomes a neuron vs a muscle cell during development?"

Different answers → different experiments

Bad Example

"What is the meaning of life?"

Too vague, no discriminative power

2Build a Corpus Excerpt

Ground your research in Brenner's wisdom. Search the corpus for relevant sections and compile them into an excerpt file.

Terminal
# Search the corpus for relevant material
brenner corpus search "cell fate determination" --limit 20
brenner corpus search "developmental biology" --limit 20
# Build an excerpt from relevant sections
brenner excerpt build --sections 58,78,161,203 > excerpt.md
# Review the excerpt
cat excerpt.md

Why excerpts matter: They provide shared context that all three agents can reference. This reduces hallucination and keeps agents grounded in the Brenner methodology.

3Write the Kickoff Prompt

The kickoff prompt should include: your research question, the excerpt, and explicit instructions for productive disagreement.

kickoff.md
# Example kickoff structure
 
## Research Question
What determines whether a neural progenitor cell commits to a
neuronal vs glial fate during CNS development?
 
## Context
I'm investigating the molecular mechanisms of cell fate determination.
The key puzzle is why genetically identical cells in the same niche
sometimes differentiate into different cell types.
 
## Relevant Brenner Wisdom
[Include your excerpt.md content here]
 
## Instructions for This Session
1. Generate 2-5 competing hypotheses (including a "third alternative")
2. Each hypothesis must specify a mechanism, not just a description
3. Design tests that can discriminate between hypotheses
4. Explicitly challenge the framing — what assumptions are we making?
 
## Constraints
- Focus on tractable mechanisms (testable in current model systems)
- Consider both cell-autonomous and non-autonomous factors
- Don't ignore the obvious — but question why it's "obvious"

4Save Your Kickoff

Save the kickoff to a file. The brenner CLI will read it when starting the session.

Terminal
# Create a sessions directory
mkdir -p sessions/RS-$(date +%Y%m%d)
# Save your kickoff
cat > sessions/RS-$(date +%Y%m%d)/kickoff.md << 'EOF'
## Research Question
[Your question here]
## Context
[Your context here]
## Relevant Brenner Wisdom
[Paste excerpt.md content]
## Instructions for This Session
[Your instructions]
EOF
Pro Tip
Include at least one "surprising constraint" in your kickoff — something that forces agents to think outside their default patterns. For example: "Assume the most obvious answer is wrong. What would that imply?"

Kickoff Ready? Save your kickoff file. In the next step, you'll use the brenner CLI to launch the session and dispatch the kickoff to all three agents.